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H2020Doctoral network2021–2024

PROTrEIN · Computational Proteomics Training European Innovative Network

Horizon 2020 — Marie Skłodowska-Curie Actions

Duration
2021-01-01 → 2024-12-31
EU contribution
€3,917,904
Participants
12
Scheme
MSCA-ITN

Lines connect the coordinator with its partners.

Results in brief

Computational Proteomics Training European Innovative Network

Mass spectrometry-based proteomics is one of the most powerful technologies for the study of the cellular proteome, protein interactions, and post-translational modifications. Although several proteomics workflows are well-established methods, the field is fast evolving with new acquisition approaches and the generation of high-content data structures. This evolution has expanded the number of applications, and mass spectrometry-based proteomics has become one of the principal platforms in the multi-omics universe. However, many of these developments require the assistance of machine-learning approaches to predict peptide properties and optimize the acquisition of proteomics datasets. These new applications often require the development of new processing algorithms to query and interpret raw mass spectrometry data, and therefore reveal hidden proteoforms, interactions, and protein modifications. The implementation of the new experimental possibilities also requires the development of interactive and highly-visual tools for the integration and representation of proteomics data with other omics datasets. Addressing these different needs is crucial to use proteomics at its full potential and thus deliver major contributions to our understanding of biological processes as well as to support the health sector with valuable information. Within this context, we need a new generation of researchers that can delve into the complexity of the computational proteomics field. Indeed, institutions and funding bodies should carve out a viable place for bioinformaticians who focus on collaborations and reward them for their abilities to navigate the myriad demands of multidisciplinary projects. PROTrEIN nurtures this new generation of computational proteomics scientists by training them on the mastering of i) the mass spectrometry raw data nature, structure, and information content, ii) mass spectrometry acquisition methods, iii) algorithms, gamification, and machine learning tools, iv) data integration and visualization, v) science communication, vi) data management, and vii) research integrity and innovation (RRI).

Data: CORDIS, © European Union

Project objective

PROTrEIN is a Training Network composed of 12 beneficiaries, and 8 partner organizations, from the academic and non-academic sectors with the mission to train a new generation of specialized bioinformaticians and improve their future employability while tackling the main challenges in computational proteomics. Mass spectrometry (MS) is one of the most powerful technologies for the study of the cellular proteome, and it is present in many translational research projects for the diagnosis and prognosis of multiple diseases, and for elucidating the mechanisms of action of drugs of medical interest. While several proteomics workflows are well established, the field is fast evolving with new acquisition methods and high-content data structures that expand the applications of the technology and make it one of the principal platforms in the multi-omics universe. Many of these developments require the assistance of artificial intelligence for the acquisition of next generation proteomics datasets, as well as the development of new processing algorithms to reveal hidden proteoforms, interactions, and protein modifications. Moreover, the usage of the new experimental possibilities requires the development of interactive and highly-visual tools for the integration and presentation of proteomics data with other omics datasets. Although addressing these different needs is crucial to deliver major contributions in our understanding of biological processes, the shortage of sufficiently trained bioinformaticians represents a major limitation. Therefore, PROTrEIN puts together an ambitious scientific and training programme to tackle both the challenges in proteomics research and the training of highly valuated professionals by mastering them on: a) the MS raw data structure and information content, b) MS acquisition methods, c) algorithms, gamification, and machine learning tools, d) data integration and visualization, e) science communication, f) data management, and g) RRI.

Original text from CORDIS.

Participants

  • FUNDACIO CENTRE DE REGULACIO GENOMICA · BarcelonaCoordinatorSpain
  • ANAXOMICS BIOTECH SL · BarcelonaSpain
  • CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS · ParisFrance
  • CONSORCIO PARA LA EXPLOTACION DEL CENTRO NACIONAL DE ANALISIS GENOMICO · BarcelonaSpain
  • EBERHARD KARLS UNIVERSITAET TUEBINGEN · TuebingenGermany
  • FH OO FORSCHUNGS & ENTWICKLUNGS GMBH · WelsAustria
  • MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV · MUNCHENGermany
  • SYDDANSK UNIVERSITET · Odense MDenmark
  • TAMPEREEN KORKEAKOULUSAATIO SR · TampereFinland
  • TECHNISCHE UNIVERSITAET MUENCHEN · MuenchenGermany
  • THERMO FISHER SCIENTIFIC (BREMEN) GMBH · BremenGermany
  • VIB VZW · ZWIJNAARDE - GENTBelgium

Links

Data: CORDIS, © European Union